Building a bio computer

Yesterday's refusal by the UK government to posthumously pardon
Alan Turing makes sad news for maths, computer science and the fight
against discrimination.

Alan Turing

But even if symbolic gestures are,
symbolically, being rebuffed, at least Turing's most
important legacy — the scientific one — is going stronger than ever. An
example is this week's announcement by scientists at the Scripps
Research Institute in California and the Technion-Israel Institute of
Technology of their development of a biological computer, based on an
idea first described by Turing in the 1930s.

We think of computers as electronic devices, but in essence a
computer is just any machine that can take an input,
manipulate it according to some specific rules, and return an output. "In contrast to electronic
computers, there are computing machines in which all four components
[input, output, hardware and software]
are nothing but molecules," says Ehud Keinan
of the Scripps Research Institute, who led the research. "For example,
all biological systems and even entire living organisms are such
computers. Every one of us is a biomolecular computer, a machine in
which all four components are molecules that 'talk' to one another
logically."

The biological computer devised by Keinan's team is made of
molecules which can effect chemical
change in one another. It consists of a solution containing DNA
molecules, DNA enzymes, which drive chemical reactions, and a molecule
called adenosine triphosphate, which can transport chemical
energy - it provides the computer's power.

When a molecule is
given as input it undergoes chemical change according to a pre-determined set of
rules that depend on the make-up of the solution. "The molecules start interacting upon one another, and we
step back and watch what happens," says Keinan. The output is another molecule with specific properties: the
result of the computation process. Programming the software in this
computer amounts to fiddling with the exact composition of the
solution in terms of DNA molecules and enzymes.

Conceptually, the biological device is based on the mother of all
computers, the Turing machine, first described in
1936 by Alan Turing. The input of this theoretical machine (there
were no real computers at that time) is a
ticker tape printed with a string of symbols which the machine can read
(a bit like the string of letters that encodes DNA). When it reaches a
symbol, the machine replaces it with something else, moves on to the
next symbol, or back to the one before, according to a set of
rules which themselves depend on the symbol it's just encountered. As
it marches through the symbols it transforms the tape, thus producing
an output. (This is an informal description — see this
Plus article for an
example and the Stanford
Encyclopedia of Philosophy for more detail.)

The biological computer was given the logos of the Scripps
Research Institute and the Technion-Israel Institute of
Technology encrypted on DNA chips as input, and it managed successfully to decrypt them.

It sounds simple, but it turns out that a Turing machine can
carry out any logical algorithm you care to throw at it, and that's
why it plays such an important role in computer science. "Our device
is based on the model of a finite state automaton, which is a
simplified version of the Turing machine," says Keinan. To test their device, his team have encrypted images on DNA
chips (these are microarrays of many very short DNA sequences) and
programmed their computer to decrypt them, which it did
successfully.

But how do biological computers compare to electronic ones? Each
step in the chemical computations is actually slower than what can be
achieved by the flow of electrons, but in compensation DNA chips can
store masses of information. When a chip is input in the machine, lots
and lots of computations are happening in parallel and that provides
speed. "Considering the fact that current [DNA] microarray technology
allows for printing millions of pixels on a single chip, the numbers
of possible images that can be encrypted on such chips is
astronomically large," says Keinan.

What's more, biological computers have the potential to interact
with biological systems and even living organisms. "No interface is
required since all components of molecular computers, including
hardware, software, input, and output, are molecules that interact in
solutions along a cascade of programmable chemical events," says
Keinan. But whatever the future for these biological devices, it's
amazing that Turing's machine, which started out as a purely
mathematical concept, now exists, almost literally, in the flesh.

The
research behind the biological computer has been published in the journal Angewandte Chemie.